Trip to Kyoto/Osaka/Naoshima/Iga-Ueno

I have a Japan Rail Pass and I'm planning on doing a 5 day trip to Kyoto, Osaka, the art-island Naoshima and the ninja village Iga-Ueno. I will head out from Tokyo and then go back to Tokyo.

Can someone please help me with laying out the train route (and ferry to Naoshima), with all necessary stops and also recommend in what order I should do these places? I'm thinking of Tokyo-Kyoto-IgaUeno-Naoshima-Osaka-Tokyo. Is this the best order to go?

Also if you know of any good and affordable hostels where I can stay in Kyoto, Naoshima and Iga-Ueno?

Thanks!

First, I need to say Tokyo-Kyoto-Osaka-Naoshima-Iga-Tokyo in 5days sound somewhat packed. You will miss many attractions in Kyoto, if you've never been there before.

The best order should be Tokyo - Kyoto - Osaka and Naoshima vice versa - Iga-ueno - Nagoya - Tokyo. You will visit Osaka again when you go back from Naoshima.

As mentioned by Ts, that would be an extremely packed trip with very little time to see each place.

Can someone please help me with laying out the train route (and ferry to Naoshima), with all necessary stops and also recommend in what order I should do these places?

Take the train to Uno Station via Okayama (about 2 hours from Osaka by shinkansen) from where it is a short ferry ride over to Naoshima by frequently departing ferries.

I would recommend to take Kyoto or Osaka as a base and visit the other three places in day trips.